Contributions ggtreeDendro

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/YuLab-SMU/ggtreeDendro

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.

I am familiar with the essential aspects of Bioconductor software management, including:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

Aug 12 '22 08:08 GuangchuangYu

Hi @GuangchuangYu

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: ggtreeDendro
Title: Drawing 'dendrogram' using 'ggtree'
Version: 0.99.1
Authors@R: c(
       person("Guangchuang", "Yu",     email = "[email protected]", role = c("aut", "cre", "cph"), 
  comment = c(ORCID = "0000-0002-6485-8781")),
       person("Shuangbin", "Xu",       email = "[email protected]",      role = "ctb", 
  comment = c(ORCID="0000-0003-3513-5362")),
       person("Chuanjie", "Zhang",       email = "[email protected]",      role = "ctb")
       )
Description: Offers a set of 'autoplot' methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using 'ggtree'. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.
Depends:
    ggtree (>= 3.5.2)
Imports:
    ggplot2
Suggests:
    aplot,
    cluster,
    knitr,
    mdendro,
    prettydoc,    
    rmarkdown,
    stats,
    yulab.utils
License: Artistic-2.0
VignetteBuilder: knitr
ByteCompile: true
Encoding: UTF-8
biocViews: Clustering, Classification, DecisionTree, Phylogenetics, Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1

Aug 12 '22 08:08 bioc-issue-bot

Please explain au and bp at end of vignette. Please begin the vignette with a discussion of the scientific relevance of the package and its suitability for the Bioc ecosystem. Thanks!

Aug 18 '22 16:08 vjcitn

We have updated the vignette. @vjcitn see https://github.com/YuLab-SMU/ggtreeDendro/commit/1dcbde559c5e1cab55d0888f81fa372986f06841.

Aug 19 '22 09:08 GuangchuangYu

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

Aug 26 '22 12:08 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ggtreeDendro to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 26 '22 12:08 bioc-issue-bot

I apologize for the delay I will have a review for you by the end of the week.

Sep 13 '22 12:09 lshep

Hello,

Please see minor comments below:

Makefile

[ ] This seems like it should not be included in the clone. Please remove and place in a .gitignore

Unit Tests

[ ] We hightly recommend adding unit tests.

man page

[ ] Please include a ggtreeDendro-package man page.

vignette

[ ] Please add 'sessionInfo()` to the end of the vignette.

R code

[ ] Please remove wgcna.R. If it is not currently being used or exported please remove until it is ready to be exported to the user.
[ ] Should the functions have any argument checking?

Please comment and push changes when ready. Cheers

Sep 16 '22 15:09 lshep

Makefile

[ ] This seems like it should not be included in the clone. Please remove and place in a .gitignore.

We think Makefile is helpful to the developers working on the terminal. It can be included in github by placing it in the .Rbuildignore meaning it will be ignored in building the package. PS: We have several Bioconductor packages that contains the Makefile in the git repo for development purpose.

Unit Tests

[x] We hightly recommend adding unit tests.

added

man page

[x] Please include a ggtreeDendro-package man page. vignette

added

[x] Please add 'sessionInfo()` to the end of the vignette.

added

R code

[x] Please remove wgcna.R. If it is not currently being used or exported please remove until it is ready to be exported to the user.

removed as suggested.

[x] Should the functions have any argument checking?

This is mainly rely on the ggtree package.

Sep 21 '22 09:09 GuangchuangYu

@lshep almost all the issues had been solved.

Sep 21 '22 09:09 GuangchuangYu

Could you please push your changes to git.bioconductor.org and trigger the new build report for review. See previous comment

Oct 04 '22 13:10 lshep

Received a valid push on git.bioconductor.org; starting a build for commit id: 685ae8639bef55239acd20426a084d81872c2e88

Oct 06 '22 05:10 bioc-issue-bot

@lshep done.

Oct 06 '22 05:10 GuangchuangYu

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ggtreeDendro to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 06 '22 05:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: ee40b8c21759b0d468253143cf4a77f57f4cce44

Oct 07 '22 02:10 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ggtreeDendro to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 07 '22 02:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: fa42a4b58f6f9bd4e2d7ddc333da1df57435b2b7

Oct 07 '22 02:10 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ggtreeDendro to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 07 '22 02:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 7c15550b39ba088e236e3182344c59b277aabd22

Oct 08 '22 08:10 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ggtreeDendro to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 08 '22 08:10 bioc-issue-bot

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

Oct 14 '22 13:10 bioc-issue-bot

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/GuangchuangYu.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("ggtreeDendro"). The package 'landing page' will be created at

https://bioconductor.org/packages/ggtreeDendro

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Oct 17 '22 12:10 lshep

Contributions Contributions copied to clipboard

ggtreeDendro

Makefile

Unit Tests

man page

R code

Contributions
Contributions copied to clipboard